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Protocols

DELTA-BLAST specifications

Information


Unique identifier OMICS_14481
Name DELTA-BLAST
Alternative name Domain Enhanced Lookup Time Accelerated BLAST
Interface Web user interface
Restrictions to use None
Input data Accession number(s), gi(s), or FASTA sequence(s)*
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • Protein BLAST

Maintainer


  • person_outline Grzegorz Boratyn

Publication for Domain Enhanced Lookup Time Accelerated BLAST

DELTA-BLAST citations

 (1433)
call_split

Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

2018
MBio
PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] analyzed using the basic local alignment search tool (BLAST) from the National Center for Biotechnology Information (NCBI) (). BLAST searches were conducted at the amino acid level using the protein-protein BLAST (blastp) function to query nonredundant protein sequences. […]

call_split

Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content

2018
Sci Rep
PMCID: 5943316
PMID: 29743515
DOI: 10.1038/s41598-018-25364-1
call_split See protocol

[…] Orthologous gene pairs between each genome pair were identified based on reciprocal best hits using the protein-protein BLAST service Blastp (https://blast.ncbi.nlm.nih.gov/Blast.cgi), with criteria of E <10−5, 80% minimum residues that could be aligned, and 30% identity. Protein sequences encoded by identified […]

library_books

Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium

2018
PLoS One
PMCID: 5942774
PMID: 29742107
DOI: 10.1371/journal.pone.0195869

[…] COG categories for all groups were assigned based on a protein BLAST search against the 2014 COG database with e-value and identity cutoffs of 1e-5 and 40% respectively. In the case of protein sequences from the metagenomic sample, only those with a lengt […]

library_books

Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

2018
BMC Genomics
PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] The genes involved in specific metabolic pathways were investigated and annotated in three steps. Firstly, protein BLAST against F. solaris protein coding amino acid sequences with corresponding amino acid sequences of P. tricornutum and T. pseudonana were performed. The query sequences were collected from […]

library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] ed genomes and the downloaded S. ureae DSM 2281 genome. Next, the protein sequences were individually compared for each genome using the BLASTp command from the BLAST+ software [] against the created protein BLAST database. The output showed if the gene in the query genome were present in all the other database genomes, and how related they were to each other. This resulted in a raw data file for […]

library_books

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose utilizing derivatives 8b and 2032

2018
Biotechnol Biofuels
PMCID: 5930841
PMID: 29743953
DOI: 10.1186/s13068-018-1116-x

[…] ORFs encode proteins that have either apparent sequence homology to proteins with defined functions in other organisms or identifiable conserved domains. The remaining 41 ORFs match to “hypothetical protein” BLAST hits from other organisms. Most plasmid genes have an ATG start codon, except for rare cases of well-predicted ORFs (i.e., highly homologous to other bacteria) that start with GTG or TT […]

Citations

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DELTA-BLAST institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
DELTA-BLAST funding source(s)
This research was supported by the Intramural Research Program of the NIH, National Library of Medicine.

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